Juglone was first preliminary purified by back extraction (BE) which also completed the sustainability of microemulsion as a solvent for extraction of juglone in J. mandshurica Maxim. branches. Then, magnetic solid phase extraction (MSPE) based on bubble column (BC) was proposed to further purify the juglone, GO/ND/Fe3O4 as adsorbent, which broke through the limitation that MSPE is only suitable for trace enrichment. Thus, a BE combined with MSPE based on BC (BE-MSPE/BC) technology to separate and purify juglone from J. mandshurica Maxim. was developed. Under the optimal conditions (optimal adsorption conditions: 0.5 h of adsorption time, 30 mg/mL of solid-liquid ratio, 5.5 of pH, 60 L/min of air flow; optimal desorption conditions: 0.4 h of desorption time, methanol of desorption agent, 100% of desorbent volume fraction, 8 of pH, 40 mg/mL of solid-liquid ratio, 80 L/min of air flow rate), the recovery yield and purity of juglone obtained by BE-MSPE/BC were 80.57% and 72.38%, respectively. BE-MSPE/BC, as a green separation and purification technology that can easily achieve large-scale and sustainable production, is expected to be an alternative method to separate and purify active components in biomass materials and products.